External Email - Use Caution Dear Douglas,
And can I include abs to the --grf 3 command? I read this in the tutorial: "NOTE: the "abs" for GRF is only approximate. For volumes, it may give very conservative results" Is it better to include neg or pos? Thank you! Regards, Agurne El vie, 19 feb 2021 a las 16:29, Douglas N. Greve (<dgr...@mgh.harvard.edu>) escribió: > You have to use --grf. I never computed the cache tables for volumes > > On 2/19/2021 9:58 AM, Agurne Sampedro Calvete wrote: > > External Email - Use Caution > Dear Douglas, > > I have another question regarding multiple comparisons correction: > > Can I use --cache with volume analyses? Or should I use --grf? > > > Thank you very much, > > Kind regards, > > > Agurne > > > El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (< > a.sampe...@deusto.es>) escribió: > >> Dear Douglas, >> Thank you very much ! This paper is very helpful. >> Regards, >> >> Agurne >> >> >> >> >> >> Neuropsychology of Severe Medical Conditions Research Team >> >> Dpt of Methods and Experimental Psychology >> Faculty of Psychology and Education >> >> University of Deusto >> >> neurolab.deusto.es >> <http://secure-web.cisco.com/1gAJEBCib9EW_ylULEVTDxDzASq_VMOoRAEIWgk_u4ErJ721bCC2wiEnNjrODzdkLXlIUmUsYnhRRjqDLlF1-Bcqys-mlDb_B2aTcm6ye1Dz08XxAm-e9QCfnFqpX3YHhkIc2TwFKsIgxRQHJTeEGrtW6m1ChKXBspuFtzKRQDbCSxIQwo8tPHgJQdt9teXZw8JgsVDegLEiWNU5Irfgx1a21XBWZK-Milh5gONHp111_8KEVyVoe2qdUfPqrPAclArlqk37HtX-_zSCMbxRkHQ/http%3A%2F%2Fneurolab.deusto.es%2F> >> >> >> >> Avda. de las Universidades 24, >> >> 48007, Bilbao (Spain) >> >> Phone: +34 944139000 (ext. 3015) >> >> >> El mar, 9 feb 2021 a las 17:55, Douglas N. Greve (<dgr...@mgh.harvard.edu>) >> escribió: >> >>> Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 >>> of this paper >>> >>> False positive rates in surface-based anatomical analysis >>> Douglas N. Greve a, b, * , Bruce Fischl a, b >>> >>> On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote: >>> >>> External Email - Use Caution >>> Dear Douglas, >>> >>> So, as far as I understand you, if I use a smoothing of 15 I can use a >>> --cache of 2 in thickness analysis, but I should use a higher --cache for >>> volume, such as 3. Is that correct? >>> And would you recommend me using another smoothing level? >>> >>> Thank you very much for your help. >>> Kind regards, >>> >>> Agurne >>> >>> El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (< >>> dgr...@mgh.harvard.edu>) escribió: >>> >>>> That is ok for thickness, but not for volume >>>> >>>> On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote: >>>> >>>> External Email - Use Caution >>>> Dear Douglas, >>>> >>>> I am doing both thickness and GM volume analyses. I am using a >>>> smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too >>>> low? And would a --cache of 2 be too low for both thickness and volume >>>> analyses, or would it be adequate at least for volume analyses? >>>> Thank you very much. >>>> >>>> Best regards, >>>> >>>> Agurne >>>> >>>> >>>> >>>> Neuropsychology of Severe Medical Conditions Research Team >>>> >>>> Dpt of Methods and Experimental Psychology >>>> Faculty of Psychology and Education >>>> >>>> University of Deusto >>>> >>>> neurolab.deusto.es >>>> <http://secure-web.cisco.com/13eL9VR1VrodsUjbGEsZKkii7H_4oFZ6JxkEjznjOHcNJSomvo7PoohKYqpfxYid2YLiqoCqS5t8lJJ8k7SGmRZW-Rrm49cqfk_FsYsh7lkHSA9hqJ4ZxCfKQvg098WrxcBQpfdHuiHniE4q0YxaN-oJGKdXw3at7j8wpNKKd1s0brILkj9hn70avIjpNZuR5rOGF4V_HoqoIoUMMn-Usc5TK09H0PoLHqXRJwtTE6xtDfrtLLG4yfDvmLs3bJM5JwAJWOMKclbenIec2VPBKjw/http%3A%2F%2Fneurolab.deusto.es%2F> >>>> >>>> >>>> >>>> Avda. de las Universidades 24, >>>> >>>> 48007, Bilbao (Spain) >>>> >>>> Phone: +34 944139000 (ext. 3015) >>>> >>>> >>>> El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (< >>>> dgr...@mgh.harvard.edu>) escribió: >>>> >>>>> >>>>> >>>>> On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote: >>>>> >>>>> External Email - Use Caution >>>>> Dear Freesurfer experts, >>>>> >>>>> I am doing a longitudinal repeated measures ANOVA 2x2, with two >>>>> groups (experimental vs control) and two time points (pre and post >>>>> treatment). >>>>> >>>>> I have followed the group analysis tutorial ( *MailScanner has >>>>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>>>> be* >>>>> https://secure-web.cisco.com/1uvView0TBMBZs9iGxZOYS5oZs4yszqMCsJpC17YEyDqbVzujehDeV5-EIP17-0nQe83_skIZAkP1zgTCr0iH7rjINBFd77LgCA6G0UtFivQrzwwIUh9U1OCnA73d5U77trRYP0oYNp1K6ceqym0L4lFZ6eVikzRJyGCq5gWrqcNyXJaxPXTjRzvQaZdeASnWnPGx_MKUPvmMtxTwONVVx8E75bALCvCOzwq4yFNM-y9k6S1DhhCsz67IcIf8HD1kZQ5P1As7OphUE-Os4Qodyw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 >>>>> <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29> >>>>> ), where it is suggested to do a Z Monte Carlo simulation with the >>>>> following command: >>>>> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp >>>>> 0.05\ --2spaces >>>>> However, I have two questions regarding this issue: >>>>> 1) I would like to know whether is it correct to use for example >>>>> --cache 3 or 2 instead of 4. Is it recommended? >>>>> >>>>> Is this a thickness analysis? If so, 3 is probably ok, but 2 is too >>>>> low; also depends on the smoothing level. >>>>> >>>>> 2) Is it better to use, instead of the above Z Monte Carlo simulation >>>>> command, a permutation with the following command?: mri_glmfit-sim \ >>>>> --glmdir >>>>> lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg >>>>> 1 >>>>> >>>>> The permutation will be more accurate, but at a threshold of 4, it >>>>> probably won't matter much. But the good thing about permutation is that >>>>> you can drop the threshold to 3 or 2 or even 1.3, and it will still do the >>>>> right thing. >>>>> >>>>> >>>>> Is it appropriate to use any of both? I do not know which is more >>>>> recommended or whether both are adequate so I can simply choose, for >>>>> example, the first one. >>>>> >>>>> Thank you very much in advance. >>>>> >>>>> Kind regards, >>>>> >>>>> Agurne >>>>> >>>>> >>>>> >>>>> Neuropsychology of Severe Medical Conditions Research Team >>>>> >>>>> Dpt of Methods and Experimental Psychology >>>>> Faculty of Psychology and Education >>>>> >>>>> University of Deusto >>>>> >>>>> neurolab.deusto.es >>>>> <http://secure-web.cisco.com/1UnrLWQpMMxdhKEG5HMrtIxWFxHsJTfrtXypEo9Dc-98NFX_4yPEsg2NqEqoQuReypFHAGq0aXxq1CsKiplAUMhJn3xTUmF95qk9IYP-L7373YTN8T8-RJR55wA1Gnu3iuM4MUGQwMR6SqTrWHWlhNVRjSS5BnRoz0lysXBO8ghrHRFlB-03jBzASp5QQha90nwuyk6z1jyP2lupIfhaAxZToPr7Ae2fnuSSJSl8bWpvgdWV6goduAv0Kk67utWKpRwjrBlEZcLB8IsAawzINIA/http%3A%2F%2Fneurolab.deusto.es%2F> >>>>> >>>>> >>>>> >>>>> Avda. de las Universidades 24, >>>>> >>>>> 48007, Bilbao (Spain) >>>>> >>>>> Phone: +34 944139000 (ext. 3015) >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>>>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>>>> be* >>>>> https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8DqcN9x-alKb9Yp1zETIdqJNC9Dfac-JEwAyQfXEAv87AHYQZtP34QxrANNJpG0iiJkCl1iyvCgkf-DQEVNfaf8fRfcq7CEXZ4zXokAjIE7DmyztjCAEdSRtxwZLce8AWOc1k4-aoFg3AU90hkYTeOHuW734QCHH5zxmEo0GxDKswIHL9mnGgvvPh67DLt25vUO5Y6Vul_u7gXREi1h9zwsUgjd_YyYCFTUHXmR3ZQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> >>>>> <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> *MailScanner has detected a possible fraud attempt from >>>>> "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8DqcN9x-alKb9Yp1zETIdqJNC9Dfac-JEwAyQfXEAv87AHYQZtP34QxrANNJpG0iiJkCl1iyvCgkf-DQEVNfaf8fRfcq7CEXZ4zXokAjIE7DmyztjCAEdSRtxwZLce8AWOc1k4-aoFg3AU90hkYTeOHuW734QCHH5zxmEo0GxDKswIHL9mnGgvvPh67DLt25vUO5Y6Vul_u7gXREi1h9zwsUgjd_YyYCFTUHXmR3ZQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>>> be* >>>> https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8DqcN9x-alKb9Yp1zETIdqJNC9Dfac-JEwAyQfXEAv87AHYQZtP34QxrANNJpG0iiJkCl1iyvCgkf-DQEVNfaf8fRfcq7CEXZ4zXokAjIE7DmyztjCAEdSRtxwZLce8AWOc1k4-aoFg3AU90hkYTeOHuW734QCHH5zxmEo0GxDKswIHL9mnGgvvPh67DLt25vUO5Y6Vul_u7gXREi1h9zwsUgjd_YyYCFTUHXmR3ZQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> <https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqEkNk30tKz3VJleOt5ehMd8LapXi1FBVJHWToBOBaYDrF0UI9s0vAcvi90NXpJnj3HjO8Skl_8QEAibD8VHRXVuguTEp6LzhZVqPLWqYOgfOo1VMYhfiy7HGa2eAEcMF-0V0piC7o8jLyFMgmejyssrx1Tdk7-c2y39CBqCcjvAin-nr0oAUYwJafCVwG-6Rj5mSsA_tYMAQcSCSlqSoEuxSwqVgZdCVAEVpQ57Ldw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> 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>>> https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8DqcN9x-alKb9Yp1zETIdqJNC9Dfac-JEwAyQfXEAv87AHYQZtP34QxrANNJpG0iiJkCl1iyvCgkf-DQEVNfaf8fRfcq7CEXZ4zXokAjIE7DmyztjCAEdSRtxwZLce8AWOc1k4-aoFg3AU90hkYTeOHuW734QCHH5zxmEo0GxDKswIHL9mnGgvvPh67DLt25vUO5Y6Vul_u7gXREi1h9zwsUgjd_YyYCFTUHXmR3ZQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1_eqzx9LmMcJt42ZWiXWynEDaQ6WqZ_ON1qgZBuXepyP20D1dzerubsAj2bkoprPCSkh1X5Pgc2fJ_i7OxXDRpdvomcJ0_6Yn9vuyBi6NGoYbXL-Cj7lVz_CegHtbtDf1xzMIOVt7mO83D7g9AGgoYKjCWgdu7Y78i3qNV8-1NpGeELLQ9YJSwr_pN_etQGsrnIBzFql9F8WUw1bOBy39AMhNBGRXhrjtQoKKHkNTDUCdw5zoou3E2HywUYvc-s8Lu-fetlHRcTj0smthjROCrQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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